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Four Research Teams to Beta Test Biomatters' Geneious Server Ahead of Full Release


By Uduak Grace Thomas

Biomatters announced last week that it has begun beta testing its Geneious Server software package, which is scheduled for release in September.

Research teams from the University of California, San Francisco; the University of Queensland; the Samuel Roberts Noble Foundation; and Verenium have begun testing the platform's next-generation sequencing assembly and phylogenetics modules, the company said.

One of the projects is led by David Edwards at the Australian Center for Plant Functional Genomics at the University of Queensland. The team plans to analyze the bread wheat genome – a polyploidy genome that is six times larger than the human genome — and will use the server to organize and analyze the sequence data generated from the project.

Biomatters, based in Auckland, New Zealand, said that UQ has built high-performance clusters designed specifically to assemble Illumina GAII genome sequence data and has also developed a sequence assembler known as SaSSY, which the team plans to eventually release as a plugin for Geneious Server.

Peter Meintjes, Biomatters' market development manager, told BioInform that in addition to the two-month private beta trial, the company will also conduct a public beta trial that would most likely begin in August.

He said that while the company chose the participants for the private beta trial, the public trial will be open to anyone who meets the technical requirements for Geneious Server.

Geneious Server is a software package that runs on a dedicated server and is designed to allow users of the company's Geneious Pro client to access high-performance computing capability for faster analysis.

Biomatters released its freely available Geneious 1.0, as well as its fee-based version of the software, Geneious Pro, in 2006 (BI 4/21/2006). The software integrates several open source sequence alignment tools, phylogenetic reconstruction, sequence annotation, and 3D protein structure viewing into a single package.

According to the company, Geneious Pro users can now “offload heavy data crunching” to Geneious Server, which is built for “highly intensive computing” allowing them to analyze large quantities of sequence data faster and freeing up memory space on their desktop computers.

The company recommends that customers install Geneious Server on an 8-core 64-bit Red Hat Linux computer with 24 GB of RAM. It can also run on a 4-core 64-bit computer with a minimum of 8 GB of RAM. The platform can also use Sun Grid Engine to distribute jobs on an in-house cluster.

Geneious Server supports PostgreSQL, MySQL, Microsoft SQL Server, and Oracle databases.

Meintjes said that the platform bridges the gap between bioinformaticians who are doing “high-intensity computing and developing algorithms” and biologists who “traditionally want to use these tools but don't know how to access them from the command line easily.

“Learning new methods and new parameters every time a new algorithm or program is put out is not something [biologists] want to do,” he said. “That's where we create a benefit for both the bioinformaticians who want their software used and the users who want to use the software.”

He noted that Geneious is "plug-in friendly" and the documentation to create and add plug-ins is available on Biomatter's website.

“In terms of the functionality that we will add ourselves, anything that is available under open source or GPL or in the public domain can be turned into a plug-in, so we can continue to add as much functionality as is requested by our users,” he said.

The server has three modules: a next-generation sequencing assembly module, a phylogenetics module, and a sequence analysis module.

Each module provides access to several tools for analyzing sequence data, however. “You always have access to all of the options,” Meintjes said. “We don't just shoehorn you into a specific way of doing things.”

For example, with the next-generation sequencing module, users can run multiple assemblies using tools such as BWA, Velvet, and Bowtie in parallel on different nodes in the cluster and then compare the results from the different tools.

In the phylogenetics module, in addition to bespoke alignment tools, Geneious Server includes several open source genome alignment tools such as ClustalW, MUSCLE, MAFFT, and Mauve. Furthermore, If a researcher needs to run a phylogenetics pipeline, Geneious Server provides access to tools such as PhyML, PAUP*, MrBayes, Neighbor-joining, and UPGMA.

Finally, the sequence analysis module lets users access tools like BLAST, HMMER, and Fasta and use them to locate genes and sequence motifs as well as to annotate genomes.

Meintjes noted that the system supports multiple file formats, handles data from different types of sequencers, has few black boxes, and includes author references so that users can correctly cite the algorithms they use for their analysis.

“The user never has to leave Geneious to do all this,” he said. “Instead of using a different tool in a different place with different command lines and settings, you have a consistent framework.”

Meintjes said that the company plans to create a version of Geneious Server that can be used without the Geneious Pro client but he did not say when that would be released.

He also declined to say how much the server would cost, other than to acknowledge that it would be more expensive than the Geneious Pro offering.

The company will face competition from a number of bioinformatics firms offering similar packages, including CLC Bio's Genomics Server, which integrates CLC and third-party client software and databases. In addition, a number of software firms are forgoing the server model completely in favor of cloud-based models for high-performance computing.

Founded in 2003, Biomatters currently has between 20 and 25 employees but will be looking to hire additional staff for a new office it plans to open in Newark, NJ, later this year. Meintjes said the company has plans to open additional offices on the West Coast and in Europe.

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